Perhaps they meet in an alternate universe where their worlds have collided. They start off as rivals, each thinking the other is a threat to their respective missions. But as they learn more about each other, they realize they can achieve more together and form an unbreakable alliance.
One idea could be that they are forced to team up against a common enemy who has the power to manipulate time. Black Widow's espionage skills and Wonder Woman's strength would make for an exciting combination in a race against time to stop the villain.